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annotate scripts/S01a_codons_counting.py @ 10:f62c76aab669 draft default tip

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planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
author lecorguille
date Mon, 24 Sep 2018 04:34:39 -0400
parents 04a9ada73cc4
children
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1 #!/usr/bin/env python
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2 # coding: utf-8
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3 # Author : Victor Mataigne
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5 import string, os, sys, re, random, itertools, argparse, copy, math
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6 import pandas as pd
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7 import numpy as np
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9 def buildDicts(list_codons, content, dict_genetic_code, dict_aa_classif):
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10 """ Build dictionaries with values to 0. These dictionaries are used as starting point for each sequence counting
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12 Args :
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13 list_codons (list of str) : all codons except codons-stop
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14 content (int or list) : an integer (for coutings and transitions), or an empty list (for resampling)
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15 dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
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16 dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...}
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18 Returns :
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19 dico_codons, dico_aa, dico_aatypes (dicts) : keys : codons/amico-acids/amico-acids types, values : 0 or []
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20 dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions (dicts of dicts) :
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21 actually, the three first dictionaries nested as values of keys codons/amico-acids/amico-acids
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22 """
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24 # I could have make sub-routines here.
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25 # the copy commands are mandatory, otherwise all dictionaries will reference the same variable(s)
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27 dico_codons = {}
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28 for codon in list_codons:
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29 dico_codons[codon] = copy.deepcopy(content)
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31 dico_aa = {}
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32 for aa in dict_genetic_code.keys():
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33 dico_aa[aa] = copy.deepcopy(content)
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35 dico_aatypes = {}
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36 for aatype in dict_aa_classif.keys():
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37 dico_aatypes[aatype] = copy.deepcopy(content)
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39 dico_codons_transitions=copy.deepcopy(dico_codons)
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40 for key in dico_codons_transitions.keys():
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41 dico_codons_transitions[key]=copy.deepcopy(dico_codons)
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43 dico_aa_transitions = copy.deepcopy(dico_aa)
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44 for key in dico_aa_transitions.keys():
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45 dico_aa_transitions[key]=copy.deepcopy(dico_aa)
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47 dico_aatypes_transitions = copy.deepcopy(dico_aatypes)
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48 for key in dico_aatypes_transitions.keys():
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49 dico_aatypes_transitions[key]=copy.deepcopy(dico_aatypes)
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51 return dico_codons, dico_aa, dico_aatypes, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions
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53 def viable(seqs, pos, method):
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54 """ Compute if, among a set of sequences, either at least one of the codons at the specified position has not a "-",
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55 or not any codon has a "-"
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57 Args :
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58 seqs : a list (the sequences, which must all have the same size)
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59 pos : an integer (the positions, <= len(seqs) -3)
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61 Returns:
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62 bool
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63 """
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64 codons = [seq[pos:pos+3] for seq in seqs]
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65 if method == "all":
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66 return not all("-" in codon for codon in codons)
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67 elif method == "any":
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68 return not any("-" in codon for codon in codons)
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70 # # # Function for codons, aa, aatypes Countings -------------------------------------------------------------------------------
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72 def computeAllCountingsAndFreqs(seq, list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif):
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73 """ Call all functions dedicated to the computation of occurences and frequencies of codons, amino-acids, amino-acids types
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75 Args : see sub-routines
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77 Returns : 6 dictionaries (occurences and frequencies for codons, amino-acids, amino-acids types). See sub-routines for details.
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78 """
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80 # ------ Sub-routines ------ #
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82 def codonsCountings(seq, list_codons, init_dict_codons):
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83 """ Count occurences of each codon in a sequence
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84 First reading frame only : input sequence is supposed to be an ORF
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85
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86 Args :
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87 seq (str) : the sequence
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88 list_codons (list of str) : all codons except codons-stop
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89 init_dict_codons (dict) : {codon1 : 0, codon2: 0, ...}
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91 Return :
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92 codon (dict) : codons (keys) and their occurences (values) in the sequence
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93 """
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94
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95 codons = copy.deepcopy(init_dict_codons)
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96
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97 l = len(seq)
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98
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99 if l%3 == 0: max_indice = l-3
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100 if l%3 == 1: max_indice = l-4
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101 if l%3 == 2: max_indice = l-5
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102
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103 for codon in range(0,max_indice+1,3):
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104 if "-" not in seq[codon:codon+3] :
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105 codons[seq[codon:codon+3]] += 1
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106
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107 return codons
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108
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109 def codonsFreqs(dict_codons_counts):
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110 """ Computes frequencies of each codon in a sequence
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111
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112 Args :
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113 dict_codons (dict) : the output of codonsCounting()
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114
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115 Return :
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116 codons_freqs (dict) : codons (keys) and their frequencies (values)
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117 """
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118
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119 codons_freqs = {}
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120
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121 for key in dict_codons_counts.keys():
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122 freq = float(dict_codons_counts[key])/sum(dict_codons_counts.values())
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123 codons_freqs[key] = freq
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124
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125 return codons_freqs
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126
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127 def aaCountings(dict_codons, dict_genetic_code, init_dict_aa):
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128 """ Count occurences of each amino-acid in a sequence, based on the countings of codons (1st ORF)
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129
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130 Args :
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131 dict_codons (dict) : the output of codonsCounting()
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132 dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
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133 init_dict_aa (dict) : {aa1 : 0, aa2: 0, ...}
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134
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135 Return :
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136 dict_aa (dict) : amino-acids (keys) and their occurences (values)
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137 """
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138 dict_aa = copy.deepcopy(init_dict_aa)
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139
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140 for key in dict_codons.keys():
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141 for value in dict_genetic_code.values():
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142 if key in value:
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143 dict_aa[dict_genetic_code.keys()[dict_genetic_code.values().index(value)]] += dict_codons[key]
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144
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145 return dict_aa
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146
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147 def aaFreqs(dict_aa_counts):
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148 """ Computes frequencies of each amino-acid in a sequence, based on the countings of codons (1st ORF)
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149
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150 Args :
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151 dict_aa_counts (dict) : the output of aaCountings()
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152
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153 Return :
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154 dict_aa_freqs (dict) : amino-acids (keys) and their frequencies (values)
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155 """
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156
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157 dict_aa_freqs = {}
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158
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159 for key in dict_aa_counts.keys():
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160 freq = float(dict_aa_counts[key])/sum(dict_aa_counts.values())
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161 dict_aa_freqs[key] = freq
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162
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163 return dict_aa_freqs
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164
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165 def aatypesCountings(dict_aa, dict_aa_classif, init_dict_classif):
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166 """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF)
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167
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168 Args :
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169 - dict_aa (dict) : the output of aaCountings()
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170 - dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...} )
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171 - init_dict_classif (dict) : {'polar': 0, 'apolar': 0, ...}
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172
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173 Return :
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174 dict_aatypes (dict) : amino-acids types (keys) and their occurences (values)
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175 """
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176 dict_aatypes = copy.deepcopy(init_dict_classif)
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177
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178 for key_classif in dict_aa_classif.keys():
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179 for key_aa in dict_aa.keys():
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180 if key_aa in dict_aa_classif[key_classif]:
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181 dict_aatypes[key_classif] += dict_aa[key_aa]
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182
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183 return dict_aatypes
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184
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185 def aatypesFreqs(dict_aatypes):
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186 """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF)
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187
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188 Args :
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189 dict_aatypes (dict) : the output of aatypesCountings()
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190
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191 Return :
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192 dict_aatypes_freqs : amino-acids types (keys) and their frequencies (values)
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193 """
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194 dict_aatypes_freqs = {}
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195
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196 for key in dict_aatypes.keys():
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197 freq = float(dict_aatypes[key])/sum(dict_aatypes.values())
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198 dict_aatypes_freqs[key] = freq
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199
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200 return dict_aatypes_freqs
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201
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202 # ------ The function ------ #
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203
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204 codons_c = codonsCountings(seq, list_codons, init_dict_codons)
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205 codons_f = codonsFreqs(codons_c)
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206 aa_c = aaCountings(codons_c, dict_genetic_code, init_dict_aa)
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207 aa_f = aaFreqs(aa_c)
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208 aat_c = aatypesCountings(aa_c, dict_aa_classif, init_dict_classif)
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209 aat_f = aatypesFreqs(aat_c)
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210
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211 return codons_c, codons_f, aa_c, aa_f, aat_c, aat_f
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212
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213 # # # Functions for various measures (ivywrel, ekqh...) -------------------------------------------------------------------------
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214
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215 def computeVarious(seq, dict_aa_counts, dict_aa_types):
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216 """ Call al the functions for nucleic and amino-acids sequences description
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217
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218 Args : See sub-routines for details.
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219
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220 Returns : 6 integer or floats. See sub-routines for details.
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221 """
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222
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223 # ------ Sub-routines ------ #
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224
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225 def nbCodons(seq):
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226 """ Compute the number of full codons in a sequence
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227 Arg : seq (str): the sequence
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228 Return: nb_codons (int)
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229 """
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230 l = len(seq)
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231 if l%3 == 0: nb_codons = l/3
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232 if l%3 == 1: nb_codons = (l-1)/3
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233 if l%3 == 2: nb_codons = (l-2)/3
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234 return nb_codons
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235
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236 def maxIndice(seq):
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237 """ Compute the highest indice for parsing a sequence
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238 Arg : seq (str): the sequence
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239 Return : max_indice (int)
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240 """
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241 l = len(seq)
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242 if l%3 == 0: max_indice = l-3
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243 if l%3 == 1: max_indice = l-4
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244 if l%3 == 2: max_indice = l-5
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245 return max_indice
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246
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247 def gc12Andgc3Count(seq, nb_codons, max_indice):
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248 """ Compute the frequency of gc12 in a sequence
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249 Arg : seq (str) : the sequence
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250 Return : (float)
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251 """
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252
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253 # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ?
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254 # But : involves a less readable code
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255
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256 gc12 = 0
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257 gc3 = 0
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258
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259 for i in range(0, max_indice+1,3):
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260 if seq[i] in ["c","g"]: gc12 += 1
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261 if seq[i+1] in ["c","g"]: gc12 += 1
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262 if seq[i+2] in ["c","g"] or seq[i+2] in ["c","g"]: gc3 += 1
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263
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264 return float(gc3)/nb_codons, float(gc12)/(2*nb_codons)
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265
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266 def ivywrelCount(nb_codons, dict_aa_counts):
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267 """ Compute the sum of occurences of amino-acids IVYWREL divided by the number of codons
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268
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269 Args :
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270 nb_codons (int) : the number of codons in the sequence
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271 dict_aa_counts (dict) : the output of aaCountings()
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272
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273 return : (float)
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274 """
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275
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276 IVYWREL = 0
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277
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278 for aa in ["I","V","Y","W","R","E","L"]: # Impossible to make a simple sum, in case one the aa is not in the dict keys
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279 if aa in dict_aa_counts.keys():
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280 IVYWREL += dict_aa_counts[aa]
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281
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282 return float(IVYWREL)/nb_codons
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283
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284 def ekqhCount(dict_aa_counts):
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285 """ Compute the ratio of amino-acids EK/QH
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286 Arg : dict_aa_counts (dict) : the output of aaCountings()
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287 Return : (float)
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288 """
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289 ek = 0
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290 qh = 0
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291
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292 ek = dict_aa_counts["E"] + dict_aa_counts["K"]
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293 qh = dict_aa_counts["Q"] + dict_aa_counts["H"]
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294
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295 if qh != 0:
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296 return float(ek)/qh
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297 else : return ek
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298
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299 def payresdgmCount(dict_aa_counts):
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300 """ Compute the ratio of amino-acids PASRE/SDGM
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301 Arg : dict_aa_counts (dict) : the output of aaCountings()
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302 Return : (float)
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303 """
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304 payre = 0
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305 sdgm = 0
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306
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307 for aa in ["P","A","Y","R","E"]:
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308 payre += dict_aa_counts[aa]
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309 for aa in ["S","D","G","M"]:
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310 sdgm += dict_aa_counts[aa]
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311
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312 if sdgm != 0:
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313 return float(payre)/sdgm
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314 else : return payre
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315
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316 def purineLoad(seq, nb_codons):
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317 """ Compute the purine load indice of a sequence
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318 Args :
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319 seq (str) : the sequence
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320 nb_codons (int) : the number of codons in the sequence
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321
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322 Return (float)
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323 """
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324
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325 # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ?
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326 # But : involves a less readable code
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327
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328 g12, g3, A, c12, c3, T = 0.0,0.0,seq.count("a"),0.0,0.0,seq.count("t")
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329
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330 # g3 and c3 : g and c in 3rd position of a codon
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331 s = ""
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332 for i in range(2, len(seq), 3):
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333 s += seq[i]
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334 g3 = s.count("g")
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335 c3 = s.count("c")
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336
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337 # g12 and c12 : g and c in 1st and 2d positions of a codon
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338 s = ""
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339 for i in range(0, len(seq), 3):
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340 s += seq[i]
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341 g12 = s.count("g")
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342 c12 = s.count("c")
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343 s = ""
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344 for i in range(1, len(seq), 3):
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345 s += seq[i]
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346 g12 += s.count("g")
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347 c12 += s.count("c")
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348
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349 return float(1000*(g12+g3+A-c12-c3-T))/(3*nb_codons)
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350
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351 def cvp(dict_aatypes):
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352 """ Compute the difference nb_charged_aamino_acids - nb_polar_amino_acids
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353 Return: (int)
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354 """
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355 return dict_aatypes["charged"] - dict_aatypes["polar"]
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356
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357 # ------ The function ------ #
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358
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359 nb_codons = nbCodons(seq)
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360 max_indice = maxIndice(seq)
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361 GC3, GC12 = gc12Andgc3Count(seq, nb_codons, max_indice)
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362 IVYWREL, EKQH, PAYRESDGM = ivywrelCount(nb_codons, dict_aa_counts), ekqhCount(dict_aa_counts), payresdgmCount(dict_aa_counts)
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363 purineload, CvP = purineLoad(seq, nb_codons), cvp(dict_aa_types)
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364 return GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP
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365
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366 # # # Function for codons, aa, aatypes Transitions -----------------------------------------------------------------------------
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367
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368 def computeAllBiases(seq1, seq2, dico_codons_transi, dico_aa_transi, dico_aatypes_transi, reversecode, reverseclassif) :
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369 """ Compute all biases (transisitions codon->codon, aa->-aa, aa_type->aa_type) between two sequences
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370
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371 Args : See sub-routines for details
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372
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373 Returns 3 dictionaries of dictionaries. See sub-routines for details
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374 """
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375
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376 # ------ Sub-routines ------ #
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377
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378 def codons_transitions(seq1, seq2, dico_codons_transi):
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379 """ Compute the number of transitions from a codon of a sequence to the codon of a second sequence
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380
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381 Args :
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382 seq1 (str) : the first sequence
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383 seq2 (str) : the second sequence
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384 dico_codons_transi (dict of dicts) : { codon1 : {codon1: 0, codon2 : 0, ...}, ..}
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385
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386 Return :
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387 codons_transi (dict of dicts) : the occurences of each codon to codon transition
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388 """
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389
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390 codons_transi = copy.deepcopy(dico_codons_transi)
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391
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392 for i in range(0, len(seq1), 3):
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393 # check if no indel and if len seq[i:i+3] is really 3 (check for the last codon)
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394 if viable([seq1, seq2], i, "any") and len(seq1[i:i+3]) == 3 and len(seq2[i:i+3]) == 3 :
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395 codons_transi[seq1[i:i+3]][seq2[i:i+3]] += 1
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396
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397 return codons_transi
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398
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399 def codons_transitions_freqs(codons_transitions_counts):
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400 """ Computes frequencies of codon transitions between two sequences
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401
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402 Arg :
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403 codons_transitions_counts (dict) : the output of codons_transitions()
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404
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405 Return :
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406 codons_transi_freqs (dict of dicts) : the frequencies of each codon to codon transition
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407 """
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408
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409 codons_transi_freqs = {}
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410
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411 for key in codons_transitions_counts.keys():
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412 codons_transi_freqs[key] = {}
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413 for key2 in codons_transitions_counts[key].keys():
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414 if sum(codons_transitions_counts[key].values()) != 0:
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415 freq = float(codons_transitions_counts[key][key2])/sum(codons_transitions_counts[key].values())
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416 codons_transi_freqs[key][key2] = freq
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417 else :
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418 codons_transi_freqs[key][key2] = 0
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419 return codons_transi_freqs
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420
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421 def aa_transitions(dico_codons_transi, dico_aa_transi, reversecode):
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422 """ Compute the number of transitions from an amino-acid of a sequence to the amino-acid of a second sequence
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423
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424 Args :
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425 dico_codons_transi (dict of dicts) : the codons transitions computed by codons_transitions()
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426 dico_aa_transi (dict of dicts) : { aa1 : {aa1: 0, aa2 : 0, ...}, ..}
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427 reversecode (dict) : the reversed genetic code {aa1 : [codons],...} -> {codon1: aa1, codon2: aa2, ...}
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428
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429 Return :
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430 aa_transi (dict of dicts) : the occurences of each aa to aa transition
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431 """
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432
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433 aa_transi = copy.deepcopy(dico_aa_transi)
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434
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435 for k in dico_codons_transi.keys():
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436 newk = reversecode[k]
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437 for k2 in dico_codons_transi[k].keys():
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438 newk2 = reversecode[k2]
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439 aa_transi[newk][newk2] += dico_codons_transi[k][k2]
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440
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441 return aa_transi
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442
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443 def aa_transitions_freqs(aa_transitions_counts):
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444 """ Computes frequencies of amico-acids transitions between two sequences
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445 Arg : aa_transitions_counts (dict of dicts): the output of aa_transitions()
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446 Return : aa_transi_freqs (dict of dicts) : the frequencies of each aa to aa transition
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447 """
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448
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449 aa_transi_freqs = {}
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450
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451 for key in aa_transitions_counts.keys():
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452 aa_transi_freqs[key] = {}
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453 for key2 in aa_transitions_counts[key].keys():
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454 if sum(aa_transitions_counts[key].values()) != 0:
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455 freq = float(aa_transitions_counts[key][key2])/sum(aa_transitions_counts[key].values())
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456 aa_transi_freqs[key][key2] = freq
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457 else :
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458 aa_transi_freqs[key][key2] = 0
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459 return aa_transi_freqs
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460
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461 def aatypes_transitions(dico_aa_transi, dico_aatypes_transi, reverseclassif):
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462 """ Compute the number of transitions from an amino-acid type of a sequence to the amino-acid type of a second sequence
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463
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464 Args :
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465 dico_aa_transi (dict of dicts) : the output of aa_transitions()
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466 dico_aatypes_transi (dict of dicts) : { type1 : {type1: 0, type2 : 0, ...}, ..}
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467 reverseclassif (dict) : the reversed amino-acid clasification {aa1: type, aa2: type, ...}
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468
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469 Return :
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470 aatypes_transi (dict of dicts) : the occurences of each aatype to aatype transition
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471 """
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472
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473 aatypes_transi = copy.deepcopy(dico_aatypes_transi)
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474 for k in dico_aa_transi.keys():
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475 newk = reverseclassif[k]
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476 for k2 in dico_aa_transi[k].keys():
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477 newk2 = reverseclassif[k2]
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478 aatypes_transi[newk][newk2] += dico_aa_transi[k][k2]
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479
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480 return aatypes_transi
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481
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482 def aatypes_transitions_freqs(aatypes_transitions_counts):
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483 """ Computes frequencies of amico-acids types transitions between two sequences
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484 Args : aatypes_transitions_counts (dict of dicts) : the output of aatypes_transitions()
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485 Return : aatypes_transi_freqs (dict of dicts) : the frequencies of each aatype to aatype transition
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486 """
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487
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488 aatypes_transi_freqs = {}
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489
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490 for key in aatypes_transitions_counts.keys():
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491 aatypes_transi_freqs[key] = {}
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492 for key2 in aatypes_transitions_counts[key].keys():
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493 if sum(aatypes_transitions_counts[key].values()) != 0:
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494 freq = float(aatypes_transitions_counts[key][key2])/sum(aatypes_transitions_counts[key].values())
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495 aatypes_transi_freqs[key][key2] = freq
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496 else :
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497 aatypes_transi_freqs[key][key2] = 0
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498 return aatypes_transi_freqs
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499
9
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500
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501
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502
5
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503 # ------ The function ------ #
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504
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505 codons_transitions = codons_transitions(seq1, seq2, dico_codons_transi)
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506 codons_transitions_freqs = codons_transitions_freqs(codons_transitions)
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507 aa_transitions = aa_transitions(codons_transitions, dico_aa_transi, reversecode)
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508 aa_transitions_freqs = aa_transitions_freqs(aa_transitions)
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509 aatypes_transitions = aatypes_transitions(aa_transitions, dico_aatypes_transi, reverseclassif)
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510 aatypes_transitions_freqs = aatypes_transitions_freqs(aatypes_transitions)
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511
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512 return codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs
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513
9
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514 def all_sed(codons_c, aa_c, aat_c, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transi, dico_aa_transi, dico_aatypes_transi):
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515
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516 def compute_sed(transi, counts, dico):
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517 """ Compute the substitution exchangeability disequilibrium (SED) from one species A to another B between codons/aa//aatypes couples
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518
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519 Args:
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520 transi ; dict - dictionaries of all counts of transition from codon/aa/aatype X to Y from sp A to sp B
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521 counts : dict - dictionaries of codons/aa/aatypes counts in species A
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522 dico : dict - a dictionary (nested) with all values to 0
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523
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524 """
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525 dict_sed = copy.deepcopy(dico)
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526
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527 for key in transi.keys():
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528 for key2 in transi.keys():
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529 if counts[key] != 0 and float(transi[key2][key])/counts[key] != 0.0:
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530 x = (float(transi[key][key2])/counts[key]) / (float(transi[key2][key])/counts[key])
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531 dict_sed[key][key2] = - pow(2,1-x)+1
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532 else :
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533 dict_sed[key][key2] = 'NA'
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534
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535 return dict_sed
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536
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537 codons_sed = compute_sed(codons_transitions, codons_c, dico_codons_transi)
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538 aa_sed = compute_sed(aa_transitions, aa_c, dico_aa_transi)
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539 aatypes_sed = compute_sed(aatypes_transitions, aat_c, dico_aatypes_transi)
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540
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541 return codons_sed, aa_sed, aatypes_sed
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542
5
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543 # # # Function for random resampling --------------------------------------------------------------------------------------------
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544
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545 def sampling (dict_seq, nb_iter, len_sample, list_codons, genetic_code, aa_classif, reversecode, reverseclassif):
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546 """ Resample randomly codons from sequences (sort of bootsrap)
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547
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548 Args :
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549 dict_seq (dict) : contains the species name and sequences used ( { 'sp1': seq1, 'sp2': seq2, ...}) without '-' removal
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550 nb_iter (int) : number of resampling iterations (better >= 1000)
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551 len_sample (int) : length (in codons) of a resampled sequence (better >= 1000)
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552 list_codons (list of str): all codons except codons-stop
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553 genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...}
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554 aa_classif (dict) : the types of the amino-acids : {type: [aa1, aa2, ...], ...}
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555 reversecode (dict) : the reversed genetic code : {codon1: aa1, codon2: aa2, ...}
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556 reverseclassif (dict) : the reversed amino-acid : clasification {aa1: type, aa2: type, ...}
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557
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558 Returns :
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559 codons_lst, aa_lst, classif_lst (dicts) : keys : codons/aa/aatypes, values : []
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560 codons_transitions_lst, aa_transitions_lst, classif_transitions_lst (dict of dicts) : keys : codons/aa/aatypes, values : the 3 previous dicts
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561 """
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562
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563 # Initialize empty dictionaries for countings and transitions. It's also possible to isntanciate these ones in the main() but it would make a function with ~14 parameters
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564 codons_0, aa_0, classif_0, codons_transitions_0, aa_transitions_0, classif_transitions_0 = buildDicts(list_codons, 0, genetic_code, aa_classif)
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565 codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst = buildDicts(list_codons, [], genetic_code, aa_classif)
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566
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567 # determine the max position where sampling is possible
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568 l = len(dict_seq.values()[1])
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diff changeset
569 if l%3 == 0: max_indice = l-3
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diff changeset
570 if l%3 == 1: max_indice = l-4
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571 if l%3 == 2: max_indice = l-5
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parents:
diff changeset
572
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abims-sbr
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573 # List of positions to resample
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574 viable_positions = [pos for pos in range(0,max_indice,3) if viable(dict_seq.values(), pos, "all")]
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diff changeset
575 sample_positions = np.random.choice(viable_positions, len_sample)
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abims-sbr
parents:
diff changeset
576
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abims-sbr
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diff changeset
577 # nb_iter resampled sequences
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abims-sbr
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578 for i in range(nb_iter):
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579 if (i+1)%(nb_iter/10) == 0:
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580 print " "+str( (i+1)*100/nb_iter)+"%"
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abims-sbr
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diff changeset
581
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582 seqa, seqb = "", ""
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abims-sbr
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583 for pos in sample_positions:
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abims-sbr
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584 codona, codonb = "---", "---"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
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585 # The sequence to be resampled in this position is randomly chosen ; no "-" resampled
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abims-sbr
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586 while "-" in codona :
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587 codona = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3]
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abims-sbr
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diff changeset
588 while "-" in codonb :
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589 codonb = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3]
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590 seqa += codona
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591 seqb += codonb
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592
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593 # dictionaries : frequences of codons, aa, aatypes (seq1)
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594 codons_occ_tmp, codons_freq_tmp, aa_occ_tmp, aa_freq_tmp, aatypes_occ_tmp, aatypes_freq_tmp = computeAllCountingsAndFreqs(seqa, list_codons, codons_0, aa_0, classif_0, genetic_code, aa_classif)
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595 # dictionaries frequences of transitions (seqa->seqb)
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596 codons_transitions_tmp, codons_transitions_freq_tmp, aa_transition_tmp, aa_transitions_freq_tmp, aatypes_transitions_tmp, aatypes_transitions_freq_tmp = computeAllBiases(seqa, seqb, codons_transitions_0, aa_transitions_0, classif_transitions_0, reversecode, reverseclassif)
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597
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598 # Adding occurrences in final dicts
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599 for key in codons_freq_tmp.keys():
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600 codons_lst[key].append(codons_freq_tmp[key])
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601 for key in aa_freq_tmp.keys():
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diff changeset
602 aa_lst[key].append(aa_freq_tmp[key])
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603 for key in aatypes_freq_tmp.keys():
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604 classif_lst[key].append(aatypes_freq_tmp[key])
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605
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606 # Adding occurrences in final dicts (transitions)
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607 for key in codons_transitions_freq_tmp.keys():
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608 for key2 in codons_transitions_freq_tmp[key].keys():
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609 codons_transitions_lst[key][key2].append(codons_transitions_freq_tmp[key][key2])
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610 for key in aa_transitions_freq_tmp.keys():
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611 for key2 in aa_transitions_freq_tmp[key].keys():
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612 aa_transitions_lst[key][key2].append(aa_transitions_freq_tmp[key][key2])
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613 for key in aatypes_transitions_freq_tmp.keys():
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614 for key2 in aatypes_transitions_freq_tmp[key].keys():
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diff changeset
615 classif_transitions_lst[key][key2].append(aatypes_transitions_freq_tmp[key][key2])
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diff changeset
616
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617 return codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst
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618
9
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619 def testPvalues(dict_counts, dict_resampling, nb_iter, method):
5
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620 """ Computes where the observed value is located in the expected counting distribution
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621
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622 Args :
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623 dict_counts (dict) : observed frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
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624 dict_resampling (dict) : expected frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases() within the sampling() function
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625
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626 Return :
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627 pvalue (dict, dict of dicts) : the pvalues of all observed countings (dict) and transitions (dict of dicts)
9
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628
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629
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630 pnorm computes the pvalue to have a value inferior to the observed value under a normal distribution
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631 One sided to left tail :
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632 p < 0.05 indicates significantly lower counts
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633 p > 0.95 indicates significantly higher counts
5
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634 """
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diff changeset
635
9
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636
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637 def p_resampling(obs, values, nb_iter):
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638 """ The pvalue is the proportion of bootsrapped values smaller than the observed value
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639 If p = 0.025 : 2.5% of the bootstrapped values are smaller than the observed value
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640 p < 0.025 : the obs value is most likely significantly lower.
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
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641 If p = 0.975 : 97.5% of the bootstrapped values are smaller than the observed value
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
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642 p > 0.975 the obs value is most likely significantly higher.
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643
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644 Args :
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645 obs : int or float - the observed value
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646 values : list - values of resampling (int or floats)
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647 nb_iter : int - the number of resampled values (=len(values))
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648
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649 Return :
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650 pvalue (float)
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651 """
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652
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653 num = len([x for x in values if x < obs])
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654 return float(num + 1) / (nb_iter+1)
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655
5
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656 def testPvalue(obs, exp, nb_iter):
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657 """ Compute a pvalue
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diff changeset
658
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
659 Args :
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
660 exp (list of floatsà : a list of length nb_iter, containing expected frequencies of a codon/aa/aatype at each iteration
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
661 obs (float) : the observed value
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
662 nb_iter (int) : the number of iterations for resampling
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
663
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
664 Returns :
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
665 pvalue (float)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
666 """
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
667
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
668 max_val = nb_iter-1
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
669 min_val = 0
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
670 test_val = (max_val+min_val)/2
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
671
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
672 while max_val-min_val > 1:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
673 if obs > exp[test_val]:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
674 min_val = test_val
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
675 test_val = (max_val+min_val)/2
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
676 elif obs < exp[test_val]:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
677 max_val = test_val
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
678 test_val = (max_val+min_val)/2
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
679 else:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
680 break
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
681
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
682 pvalue = float(test_val+1)/(nb_iter+1)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
683
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
684 return pvalue
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
685
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
686 # ------ The function ------ #
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
687
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
688 pvalues = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
689
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
690 for key in dict_resampling.keys():
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
691 if type(dict_resampling.values()[1]) is not dict :
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
692 if method == 'origin':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
693 pvalues[key] = testPvalue(dict_counts[key], dict_resampling[key], nb_iter)
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
694 elif method == 'pnorm':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
695 pvalues[key] = scipy.stats.norm.cdf(dict_counts[key], np.mean(dict_resampling[key]), np.std(dict_resampling[key]))
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
696 elif method == 'p_resampling':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
697 pvalues[key] = p_resampling(dict_counts[key], dict_resampling[key], nb_iter)
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
698 else :
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
699 pvalues[key] = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
700 for key2 in dict_resampling[key].keys():
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
701 if method == 'origin':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
702 pvalues[key][key2] = testPvalue(dict_counts[key][key2], dict_resampling[key][key2], nb_iter)
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
703 elif method == 'pnorm':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
704 pvalues[key][key2] = scipy.stats.norm.cdf(dict_counts[key][key2], np.mean(dict_resampling[key][key2]), np.std(dict_resampling[key][key2]))
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
705 elif method == 'p_resampling':
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
706 pvalues[key][key2] = p_resampling(dict_counts[key][key2], dict_resampling[key][key2], nb_iter)
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
707
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
708 return pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
709
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
710 def main():
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
711
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
712 # arguments
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
713 parser = argparse.ArgumentParser()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
714 parser.add_argument("sequences_file", help="File containing sequences (the output of the tool 'ConcatPhyl'")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
715 parser.add_argument("considered_species", help="The species name, separated by commas (must be the same than in the sequences_file). It is possible to consider only a subset of species.")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
716 parser.add_argument("species_for_bootstrap", help="The species which will be used for bootstrapping, separated by commas. It is possible to consider only a subset of species.")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
717 parser.add_argument("iteration", help="The number of iterations for bootstrapping (better if => 1000)", type=int)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
718 parser.add_argument("sample_length", help="The lenght of a bootstrapped sequences (better if >= 1000", type=int)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
719 args = parser.parse_args()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
720
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
721 print "\n ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
722
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
723 print "The script counts the number of codons, amino acids, and types of amino acids in sequences,"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
724 print "as well as the mutation bias from one item to another between 2 sequences.\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
725
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
726 print "Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
727 print "In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
728 print "a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
729
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
730 print " Sequences file : {}".format(args.sequences_file)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
731 print " Species retained for countings : {}\n".format(args.considered_species)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
732
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
733 print "Processing : reading input file, opening output files, building dictionaries."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
734
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
735 # make pairs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
736 list_species = str.split(args.considered_species, ",")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
737 list_species_boot = str.split(args.species_for_bootstrap, ",")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
738 pairs_list=list(itertools.combinations(list_species,2))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
739
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
740 # read sequences
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
741 sequences_for_counts = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
742 sequences_for_resampling = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
743 with open(args.sequences_file, "r") as file:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
744 for line1,line2 in itertools.izip_longest(*[file]*2):
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
745 species = line1.strip(">\r\n")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
746 sequence = line2.strip("\r\n")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
747 if species in list_species:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
748 sequences_for_counts[species] = sequence
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
749 if species in list_species_boot:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
750 sequences_for_resampling[species] = sequence
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
751
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
752 print " Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
753 print " Frequences are more representative."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
754
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
755 print "\n Indels percent :"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
756
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
757 for k,v in sequences_for_counts.items():
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
758 print " {} : {} %".format(k, float(v.count("-"))/len(v)*100)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
759
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
760 # useful dictionaries
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
761 dict_genetic_code={"F":["ttt","ttc"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
762 "L":["tta","ttg","ctt","ctc","cta","ctg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
763 "I":["att","atc","ata"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
764 "M":["atg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
765 "V":["gtt","gtc","gta","gtg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
766 "S":["tct","tcc","tca","tcg","agt","agc"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
767 "P":["cct","cca","ccg","ccc"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
768 "T":["act","acc","aca","acg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
769 "A":["gct","gcc","gca","gcg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
770 "Y":["tat","tac"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
771 "H":["cat","cac"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
772 "Q":["caa","cag"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
773 "N":["aat","aac"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
774 "K":["aaa","aag"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
775 "D":["gat","gac"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
776 "E":["gaa","gag"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
777 "C":["tgt","tgc"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
778 "W":["tgg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
779 "R":["cgt","cgc","cga","cgg","aga","agg"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
780 "G":["ggt","ggc","gga","ggg"]}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
781
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
782 dict_aa_classif={"unpolar":["G","A","V","L","M","I"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
783 "polar":["S","T","C","P","N","Q"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
784 "charged":["K","R","H","D","E"],
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
785 "aromatics":["F","Y","W"]}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
786
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
787 reversecode={v:k for k in dict_genetic_code for v in dict_genetic_code[k]}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
788 reverseclassif={v:k for k in dict_aa_classif for v in dict_aa_classif[k]}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
789
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
790 # codons list (without stop codons)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
791 nucleotides = ['a', 'c', 'g', 't']
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
792 list_codons = [''.join(comb) for comb in itertools.product(nucleotides, repeat=3)]
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
793 list_codons.remove("taa")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
794 list_codons.remove("tag")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
795 list_codons.remove("tga")
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
796
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
797 # Store already computed species + row.names in output files
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
798 index = []
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
799 index_transi = []
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
800
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
801 # Final dictionaries writed to csv files
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
802 all_codons = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
803 all_aa = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
804 all_aatypes = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
805 all_various = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
806 all_codons_transitions = {} # Not used because too much : 61*61 columns
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
807 all_aa_transitions = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
808 all_aatypes_transitions = {}
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
809
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
810 # RUN
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
811
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
812 print "\nProcessing : resampling ..."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
813 print " Parameters : {niter} iterations, {lensample} codon per resampled sequence, species used : {species}\n".format(niter=args.iteration, lensample=args.sample_length, species=args.species_for_bootstrap)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
814
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
815 codons_boot, aa_boot, aatypes_boot, codons_transi_boot, aa_transi_boot, aatypes_transi_boot = sampling(sequences_for_resampling, args.iteration, args.sample_length, list_codons, dict_genetic_code, dict_aa_classif, reversecode, reverseclassif)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
816 print " Done.\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
817
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
818 print "Processing : countings....\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
819
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
820 # Initialize empty dictionaries for countings and transitions
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
821 init_dict_codons, init_dict_aa, init_dict_classif, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions = buildDicts(list_codons, 0, dict_genetic_code, dict_aa_classif)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
822
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
823 for pair in pairs_list:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
824 p1, p2 = pair[0], pair[1]
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
825 if p1 not in index:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
826 print "Countings on {}".format(p1)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
827
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
828 p1_codons_counts, p1_codons_freqs, p1_aa_counts, p1_aa_freqs, p1_aatypes_counts, p1_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p1], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
829 p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP = computeVarious(sequences_for_counts[p1], p1_aa_counts, p1_aatypes_freqs)
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
830
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
831
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
832 p1_codons_pvalues = testPvalues(p1_codons_freqs, codons_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
833 p1_aa_pvalues = testPvalues(p1_aa_freqs, aa_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
834 p1_aatypes_pvalues = testPvalues(p1_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling')
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
835
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
836 all_codons[p1+"_obs_counts"] = p1_codons_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
837 all_codons[p1+"_obs_freqs"] = p1_codons_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
838 all_codons[p1+"_pvalues"] = p1_codons_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
839 all_aa[p1+"_obs_counts"] = p1_aa_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
840 all_aa[p1+"_obs_freqs"] = p1_aa_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
841 all_aa[p1+"_pvalues"] = p1_aa_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
842 all_aatypes[p1+"_obs_counts"] = p1_aatypes_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
843 all_aatypes[p1+"_obs_freqs"] = p1_aatypes_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
844 all_aatypes[p1+"_pvalues"] = p1_aatypes_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
845 all_various[p1] = [p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP]
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
846
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
847 index.append(p1)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
848
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
849 if p2 not in index:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
850 print "Countings on {}".format(p2)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
851
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
852 p2_codons_counts, p2_codons_freqs, p2_aa_counts, p2_aa_freqs, p2_aatypes_counts, p2_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p2], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
853 p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP = computeVarious(sequences_for_counts[p2], p2_aa_counts, p2_aatypes_freqs)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
854
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
855 p2_codons_pvalues = testPvalues(p2_codons_freqs, codons_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
856 p2_aa_pvalues = testPvalues(p2_aa_freqs, aa_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
857 p2_aatypes_pvalues = testPvalues(p2_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling')
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
858
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
859 all_codons[p2+"_obs_counts"] = p2_codons_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
860 all_codons[p2+"_obs_freqs"] = p2_codons_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
861 all_codons[p2+"_pvalues"] = p2_codons_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
862 all_aa[p2+"_obs_counts"] = p2_aa_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
863 all_aa[p2+"_obs_freqs"] = p2_aa_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
864 all_aa[p2+"_pvalues"] = p2_aa_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
865 all_aatypes[p2+"_obs_counts"] = p2_aatypes_counts
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
866 all_aatypes[p2+"_obs_freqs"] = p2_aatypes_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
867 all_aatypes[p2+"_pvalues"] = p2_aatypes_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
868 all_various[p2] = p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
869
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
870 index.append(p2)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
871
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
872 if (p1, p2) not in index_transi and p1 in sequences_for_counts and p2 in sequences_for_counts:
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
873 print "Countings transitions between {} and {}".format(p1, p2)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
874 codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs = computeAllBiases(sequences_for_counts[p1], sequences_for_counts[p2], dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions, reversecode, reverseclassif)
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
875
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
876 # Ajout
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
877 codons_sed, aa_sed, aatypes_sed = all_sed(p1_codons_counts, p1_aa_counts, p1_aatypes_counts, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions)
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
878
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
879 index_transi.append((p1,p2))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
880
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
881 p1p2_codons_pvalues = testPvalues(codons_transitions_freqs, codons_transi_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
882 p1p2_aa_pvalues = testPvalues(aa_transitions_freqs, aa_transi_boot, args.iteration, 'p_resampling')
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
883 p1p2_aatypes_pvalues = testPvalues(aatypes_transitions_freqs, aatypes_transi_boot, args.iteration, 'p_resampling')
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
884
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
885 all_codons_transitions[p1+">"+p2+"_obs_counts"] = codons_transitions
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
886 all_codons_transitions[p1+">"+p2+"_obs_freqs"] = codons_transitions_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
887 all_codons_transitions[p1+">"+p2+"_pvalues"] = p1p2_codons_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
888 all_aa_transitions[p1+">"+p2+"_obs_counts"] = aa_transitions
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
889 all_aa_transitions[p1+">"+p2+"_obs_freqs"] = aa_transitions_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
890 all_aa_transitions[p1+">"+p2+"_pvalues"] = p1p2_aa_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
891 all_aatypes_transitions[p1+">"+p2+"_obs_counts"] = aatypes_transitions
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
892 all_aatypes_transitions[p1+">"+p2+"_obs_freqs"] = aatypes_transitions_freqs
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
893 all_aatypes_transitions[p1+">"+p2+"_pvalues"] = p1p2_aatypes_pvalues
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
894
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
895 all_codons_transitions[p1+">"+p2+"_sed"] = codons_sed
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
896 all_aa_transitions[p1+">"+p2+"_sed"] = aa_sed
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
897 all_aatypes_transitions[p1+">"+p2+"_sed"] = aatypes_sed
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
898
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
899 index_transi.append((p1, p2))
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
900
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
901 print "\n Done.\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
902
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
903 print "Processing : creating dataframes ..."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
904
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
905 frame_codons = pd.DataFrame(all_codons).T.astype('object')
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
906 frame_aa = pd.DataFrame(all_aa).T.astype('object')
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
907 frame_aatypes = pd.DataFrame(all_aatypes).T.astype('object')
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
908
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
909 frame_codons_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_codons_transitions.items()}).unstack()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
910 frame_codons_transitions.columns = frame_codons_transitions.columns.map('>'.join)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
911
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
912 frame_aa_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aa_transitions.items()}).unstack()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
913 frame_aa_transitions.columns = frame_aa_transitions.columns.map('>'.join)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
914
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
915 frame_aatypes_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aatypes_transitions.items()}).unstack()
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
916 frame_aatypes_transitions.columns = frame_aatypes_transitions.columns.map('>'.join)
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
917
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
918 frame_various = pd.DataFrame(all_various).T
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
919 frame_various.columns = ["GC3","GC12","IVYWREL","EKQH","PAYRESDGM","purineload", "CvP"]
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
920
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
921 frame_codons.index.name, frame_aa.index.name, frame_aatypes.index.name = "Species", "Species","Species"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
922 frame_aa_transitions.index.name, frame_aatypes_transitions.index.name, frame_various.index.name = "Species","Species","Species"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
923
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
924 print "Writing dataframes to output files ...\n"
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
925
9
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
926 frame_codons.round(8).to_csv("codons_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
927 frame_aa.round(8).to_csv("aa_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
928 frame_aatypes.astype('object').round(8).to_csv("aatypes_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
929 frame_codons_transitions.round(8).to_csv("codons_transitions_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
930 frame_aa_transitions.round(8).to_csv("aa_transitions_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
931 frame_aatypes_transitions.round(8).to_csv("aatypes_transitions_freqs.csv", sep=",", encoding="utf-8")
04a9ada73cc4 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
abims-sbr
parents: 5
diff changeset
932 frame_various.round(8).to_csv("gc_and_others_freqs.csv", sep=",", encoding="utf-8")
5
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
933
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
934 print "Done."
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
935
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
936 if __name__ == "__main__":
0ba551449008 planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
abims-sbr
parents:
diff changeset
937 main()